{"id":"W4404902753","doi":"10.1186/s13059-024-03441-1","title":"SMART: spatial transcriptomics deconvolution using marker-gene-assisted topic model","year":2024,"lang":"en","type":"article","venue":"Genome biology","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; St. Paul's Hospital; University of British Columbia Hospital","funders":"","keywords":"Deconvolution; Biology; Computational biology; Context (archaeology); Identification (biology); Transcriptome; Gene; Cell type; Gene expression; Genetics; Cell; Computer science; Algorithm","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001693724,0.0002407864,0.00022294,0.00009542567,0.0001103464,0.00004192352,0.000215621,0.0004014958,0.00004242635],"category_scores_gemma":[0.00001270376,0.000237016,0.0001949316,0.0001013921,0.0001237312,0.000005939507,0.00004861733,0.0001474727,0.00001937077],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006562987,"about_ca_system_score_gemma":0.0002010105,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001790514,"about_ca_topic_score_gemma":0.0002097041,"domain_scores_codex":[0.9985599,0.00007850696,0.000318367,0.0005717903,0.00006174394,0.0004096802],"domain_scores_gemma":[0.9994989,0.00000989773,0.00003996703,0.0003003785,0.00005208856,0.00009879318],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001047554,0.0000394685,0.001364641,0.00003870902,0.0001006739,0.000004933357,0.00005913679,0.0005671697,0.9910989,0.0002429447,0.00004334758,0.006335358],"study_design_scores_gemma":[0.003062745,0.00138325,0.01663556,0.00007630846,0.0004561293,0.0003890207,0.00007264531,0.3916431,0.4110792,0.003058967,0.1697709,0.002372192],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7957501,0.003615682,0.1986673,0.00008918241,0.001101251,0.0001633248,0.0001240823,0.00004830584,0.000440769],"genre_scores_gemma":[0.994013,0.0003572544,0.003723565,0.00025676,0.000536819,0.00001465121,0.0005444808,0.00004429992,0.0005091694],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5800197,"threshold_uncertainty_score":0.9665233,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03064309977635044,"score_gpt":0.2615926337446557,"score_spread":0.2309495339683053,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}